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Themed collection Physical Foundations of Protein Folding

7 articles
Perspective

Probing molecular kinetics with Markov models: metastable states, transition pathways and spectroscopic observables

Markov (state) models are useful for identifying metastable conformations from simulated data, to investigate ensembles of folding pathways and to link MD simulation with kinetic experiments.

Graphical abstract: Probing molecular kinetics with Markov models: metastable states, transition pathways and spectroscopic observables
From the themed collection: Physical Foundations of Protein Folding
Perspective

Diffusion models of protein folding

Descriptions of protein folding as diffusion along low-dimensional reaction coordinates capture the observed simulation dynamics and help interpret single-molecule experiments.

Graphical abstract: Diffusion models of protein folding
From the themed collection: Biophysics and biophysical chemistry in PCCP
Perspective

Coarse-grained force field: general folding theory

UNRES force field is a tool with which to carry out ab initio simulations of protein folding.

Graphical abstract: Coarse-grained force field: general folding theory
From the themed collection: Physical Foundations of Protein Folding
Paper

Protonation/deprotonation effects on the stability of the Trp-cage miniprotein

The effect of protonating the aspartic acid on the Trp-cage folding/unfolding equilibrium is studied by explicit solvent molecular dynamics simulations.

Graphical abstract: Protonation/deprotonation effects on the stability of the Trp-cage miniprotein
From the themed collection: Physical Foundations of Protein Folding
Paper

Estimation of protein folding free energy barriers from calorimetric data by multi-model Bayesian analysis

A global multi-model Bayesian analysis of scanning calorimetry data allows a high-sensitivity, robust and model-independent estimation of thermodynamic protein folding barriers.

Graphical abstract: Estimation of protein folding free energy barriers from calorimetric data by multi-model Bayesian analysis
From the themed collection: Physical Foundations of Protein Folding
Paper

Integrated prediction of protein folding and unfolding rates from only size and structural class

A simple physics-based model that predicts protein folding and unfolding rates using size and structural class as only specific input.

Graphical abstract: Integrated prediction of protein folding and unfolding rates from only size and structural class
From the themed collection: Physical Foundations of Protein Folding
Paper

Why not consider a spherical protein? Implications of backbone hydrogen bonding for protein structure and function

Comparing artificial (orange) and quasi-spherical (purple) protein models, hydrogen bonding leads to protein-like cavities for ligand-binding and interfaces for protein/DNA-binding.

Graphical abstract: Why not consider a spherical protein? Implications of backbone hydrogen bonding for protein structure and function
From the themed collection: Physical Foundations of Protein Folding
7 articles

About this collection

We are delighted to present a high-profile themed collection on the Physical Foundations of Protein Folding. This themed collection, Guest Edited by Modesto Orozco (IRB Barcelona), contains a mix of exciting ‘Perspective’ review articles and cutting-edge research papers. Watch out for more PCCP articles on this theme which will be added to this collection throughout 2011.

This special themed collection emphasizes the recent advances from all three approaches in protein folding: experiment, theory and simulations. It also provides a platform for discussing interesting concepts in protein folding and the direction this field will take in the future.

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